There is a conflict of jurisdiction between the maritime environmental dispute settlement mechanism and the WTO dispute settlement mechanism, which can lead to conflicts in practice, especially with regard to free trade. This paper therefore analyses the EC-Chile Swordfish case, in which both parties to the dispute submitted their cases to both the UN Tribunal for the Law of the Sea and the WTO panel procedure, and finds that the conflict of jurisdiction between the two mechanisms arises because of the conflicting concepts of their rules and the lack of specific provisions that make them equivalent in effect. As a result, it was not possible to exclude the jurisdiction of the other party, which could lead to different outcomes and a new impasse in dispute resolution. It is therefore important to harmonise the conflicting principles of the marine environment and free trade, and to establish a coordinating body between the two mechanisms in order to better resolve marine environmental disputes and ultimately help China to deal with such conflicts and establish its own environmental and trade regime.